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Review
. 2011 Dec;107(6):487-95.
doi: 10.1038/hdy.2011.43. Epub 2011 Jun 15.

Origin and evolution of SINEs in eukaryotic genomes

D A Kramerov  1 , N S Vassetzky
Affiliations
Review

Origin and evolution of SINEs in eukaryotic genomes

D A Kramerov et al. Heredity (Edinb). 2011 Dec.

Abstract

Short interspersed elements (SINEs) are one of the two most prolific mobile genomic elements in most of the higher eukaryotes. Although their biology is still not thoroughly understood, unusual life cycle of these simple elements amplified as genomic parasites makes their evolution unique in many ways. In contrast to most genetic elements including other transposons, SINEs emerged de novo many times in evolution from available molecules (for example, tRNA). The involvement of reverse transcription in their amplification cycle, huge number of genomic copies and modular structure allow variation mechanisms in SINEs uncommon or rare in other genetic elements (module exchange between SINE families, dimerization, and so on.). Overall, SINE evolution includes their emergence, progressive optimization and counteraction to the cell's defense against mobile genetic elements.

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Figures

Figure 1
Figure 1
SINE structure examples. (a) Ther-1 is a tRNA-derived CORE SINE of stringent recognition group (Gilbert and Labuda, 1999); (b) Ped-1, 5S rRNA-derived SINE of stringent recognition group (with bipartite LINE region; Gogolevsky et al., 2008); (c) B1, 7SL RNA-derived quasi-dimeric SINE of relaxed recognition group (Labuda et al., 1991); (d) CAN, tRNA-derived SINE of relaxed recognition group with a variable polypyrimidine region (Vassetzky and Kramerov, 2002); (e) MEG-RS, simple 5S rRNA-derived SINE of relaxed recognition group (Gogolevsky et al., 2009); (f) MEN, dimeric tRNA/7SL RNA (heterodimeric) SINE of relaxed recognition group (Serdobova and Kramerov, 1998).
Figure 2
Figure 2
SINEs in the genome of wallaby mobilized by different LINEs: Ther-1 (MIR), L2; Ther-2 (MIR3), L3; Mar-1, Bov-B (Gilbert and Labuda, 1999); Mar-3 (WSINE1), L1 (Munemasa et al., 2008). The LINE partners of Mac-1 (WALLSI2; Munemasa et al., 2008) and WALLSI4 (Jurka et al., 2005) remain to be identified. Alternative SINE names are given in parentheses.
Figure 3
Figure 3
Mechanisms of SINE variation during their life cycle.
Figure 4
Figure 4
The de novo emergence of SINEs in placental mammals. The mammalian tree corresponds to the TimeTree Knowledge Base (Hedges et al., 2006).
Figure 5
Figure 5
Length distribution of SINE families (without tail; plotted for 125 elements).
See this image and copyright information in PMC

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